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Pairwise sequence alignments & BLAST BLAST Lab
Meg Staton edited this page Sep 24, 2016
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##Goals
- Understand how sequence alignments are generated and scored
- Understand substitution matrices (used for scoring sequence alignments)
- Learn to blast on newton
- Start submitting jobs to the newton queue
- Construct a dotplot from a simple word (for example “EPP622” against itself)
- How biology is used to do smarter sequence alignment scoring (for both nucleotides and amino acids)
- What are PAM and BLOSUM matrices? What are they used for?
- Gap open vs gap extension penalties - why are they different?
- Differences in needleman and wunsch vs smith and waterman
- Differences in global and local alignments
- What does heuristic mean?
- BLAST is it heuristic or guaranteed to give you best results?
- What does the acronym BLAST stand for?
- What is an E value?
##Materials
##Readings Camacho et al. 2010 BLAST+: architecture and applications